RetrogeneDB ID:

retro_pcap_36

Retrocopy
location
Organism:Hyrax (Procavia capensis)
Coordinates:GeneScaffold_1698:9446..9788(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP1
Ensembl ID:ENSPCAG00000014595
Aliases:None
Description:ribosomal protein, large, P1 [Source:HGNC Symbol;Acc:10372]


Retrocopy-Parental alignment summary:






>retro_pcap_36
ATAGCCTCTGTCTCTGACCTGTGCTGCATCTTCTTGGCCCTCATCCTGCATGACAACAATAAGGTGACCATGAAGGAGGA
TAAGATCACAGCCCTCATTAAAGCAGCCTGTGTAAATGTCAGACCTTCCTGGCCTAGCTTGTTTGCAAAGGCTCTGGCCA
GCATCAACAAGGGGAGCCTCATGTGCTGGGTAGAGGCTAGTGGACCTGTCCCAGCAGCCAGCACTGCACCAGCAGGGGAT
GTTCCCTCTCCACCACTGCTGCCTCAGCTTAGGATTAAAACATAGAATAAAGAATGAAGAATCTGAAGAGTCCATAATGA
CATGAGCTTTGGTCTTTCTGAC

ORF - retro_pcap_36 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.86 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMASVSELACIYSALILHDD-EVTVTEDKINALIKAAGVNVEPFWPGLFAKALANVNIGSLICNVGAGGPA
.ASVS.L.CI..ALILHD...VT..EDKI.ALIKAA.VNV.P.WP.LFAKALA..N.GSL.C.V.A.GP.
RetrocopyIASVSDLCCIFLALILHDNNKVTMKEDKITALIKAACVNVRPSWPSLFAKALASINKGSLMCWVEASGPV
ParentalPAPGAAPAG-GPAPSTAAAPAEEKKVE-AKKEESEES-DDDMGFGLFD
PA...APAG.G...ST.AA.A.....E..K.EESEES...DM.FGL.D
RetrocopyPAASTAPAG<GCSLSTTAASA*D*NIE<IKNEESEES<HNDMSFGLSD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Procavia capensis was not studied using RNA-Seq expression data.
Procavia capensis was not studied using ChIP-Seq data.
Procavia capensis was not studied using EST data.
Procavia capensis was not studied using FANTOM5 data.
retro_pcap_36 was not experimentally validated.

Retrocopy orthology:
Procavia capensis does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:
Parental genes homology involve 20 parental genes, and 182 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000183204 retrocopies
Callithrix jacchus ENSCJAG0000003291919 retrocopies
Equus caballus ENSECAG000000085424 retrocopies
Homo sapiens ENSG0000013781818 retrocopies
Gorilla gorilla ENSGGOG0000000398013 retrocopies
Latimeria chalumnae ENSLACG000000126301 retrocopy
Macropus eugenii ENSMEUG000000152776 retrocopies
Myotis lucifugus ENSMLUG0000001054233 retrocopies
Macaca mulatta ENSMMUG000000148887 retrocopies
Monodelphis domestica ENSMODG000000092091 retrocopy
Mustela putorius furoENSMPUG0000000020413 retrocopies
Mus musculus ENSMUSG000000078926 retrocopies
Oryctolagus cuniculus ENSOCUG000000150878 retrocopies
Otolemur garnettii ENSOGAG0000002964119 retrocopies
Procavia capensis ENSPCAG00000014595 7 retrocopies
Pongo abelii ENSPPYG000000066015 retrocopies
Pan troglodytes ENSPTRG000000072281 retrocopy
Rattus norvegicus ENSRNOG000000119556 retrocopies
Rattus norvegicus ENSRNOG000000138743 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000278938 retrocopies



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